Objects can be custom colored in Jmol using the color (or colour) command:color [object] [color or color scheme]

[color] is specified as decimal [red,green,blue] or hexadecimal [xRRGGBB] triplets.
It can also be a JavaScript color name, a RasMol color name, or a Jmol color name.
(For the default colors and color values used in Jmol, see tables below.)

[color scheme] is specified using pre-defined terms detailed on this page.

Applies color to each atom of the object according to element, as shown in the tables below. Backbone displays such as ribbons, cartoons, etc. are rendered in the color of alpha carbons for proteins, phosphorus for nucleic acids.

Default element colors, by periodic table:

Hover over any element to see more information.
Click on an element to move to the same information in the Atomic Numbers table below.

Default element colors, by atomic number:

“CPKnew” scheme applies only to Rasmol v. 2.7.3
(or later); only differences with classic CPK are shown.
Note: CPKnew for unknown atoms is
FA1691,
slightly different from CPK
FF1493,
but has been omitted for clarity in the table.

'amino' renders each of the 20 standard amino acid residues
(as well as Asx and Glx) in a certain color,
along with one additional color for anything else (including nucleotides, solvents, and non-amino ligands).
Some colors are shared by two or more amino acids with similar properties.

'shapely' uses a different set of colors for amino acids
(each one different) and also colors differentially the 6 kinds
of nucleotides.

Renders each chain in the structure in a different color.
This color scheme is particularly useful for distinguishing the parts
of a multimeric structure or the individual DNA strands of a double helix.
Atoms in HETERO groups (PDB files only) are colored in a different shade
than those in ATOM records: darker for chains A-Q,S, lighter for chains R,T-Z.

The PDB format
requires
that each chain ID be a non-blank alphanumeric character. Thus, a
maximum of 62 chains is permitted in a single model within a PDB file
(26 times 2, for upper and lower case letters A-Z, plus 10, for chain IDs 0-9).
An example with 62 chains is 2zkr. PDB files obtained before
remediation of the database may have chain IDs that are blank or not
alphanumeric (e.g. punctuation characters) but this is no longer
permitted. Although chain 'A' is the same color as chain 'a' (and so forth),
they may be selected independently (see the
set chainCaseSensitive command).

Uses different colors to distinguish six types of protein secondary
structures (three types of helices, beta strands or sheets, turns, and loops) and
DNA vs. RNA. The secondary structure is either read from the PDB file
(HELIX and SHEET records), if available, or determined using an algorithm.

If a chain has a break in it, the 2 pieces of the chain are recognized as separate polymers, and hence each one is colored independently with the full color range, despite the fact that both parts are designated with the same chain ID in the coordinate file.

Again, the numbering of groups in the file is irrelevant.

HETERO groups may participate in a polymer, depending upon how the PDB/mmCIF file is marked up, and as long as they have a backbone pattern that Jmol can recognize as a sequence of individual units.

RasMol/Chime note:
In RasMol/Chime, group index is relative to the full chain, while in Jmol
it is relative to the currently selected groups of the chain.
In addition, the "set hetero" command is not implemented in Jmol.
If you want to exclude "hetero" groups, then do not select them.

Colors each atom, using a bwr gradient, according to the "temperature
factor" (B factor, or Debye-Waller factor) value stored in the PDB
or mmCIF file. Typically this gives a measure of the mobility or
uncertainty of a given atom's position. A high crystallographic
B factor may indicate an incorrect structure.

'fixedTemperature':
the factor is referred to an absolute scale of 0 to 100.

'relativeTemperature':
the color is relative to the lowest and highest B factor values
within the file (not within the selection).

'relativeTemperature' after 'set rangeSelected on':
the color is relative to the lowest and highest B factor values
within the currently selected part of the model.

Note: The temperature factor fields in a PDB file are sometimes used
by the file creator to indicate any other characteristic of the atoms
in the model.

RasMol/Chime note:
In RasMol and Chime, 'temperature' (the only option available) uses
also a relative scale, but with a reverse rainbow gradient (bgyor).
In Jmol, 'temperature' does the same as 'relativeTemperature'.

Colors atoms based on their formal charge, or ionic state.
Uses a restricted rwb gradient: tints of red for anions,
tints of blue for cations, white for uncharged atoms.
The range of values handled by Jmol for formal charge is -4 through +7,
in an absolute scale.

Colors atoms based on their partial charge, or electron density.
Uses a rwb gradient: tints of red for high electron density,
tints of blue for low electron density, white for neutral.
The range of values for partial charge is adjusted to the minimum and
maximum values present in the file (i.e., a scale relative to the file
values is used, but not to values in the selected set of atoms).

RasMol/Chime note:
In RasMol and Chime, 'charge' (the only option available) is meant for
PDB files that hold partial charges in the B factor columns, and uses
a direct rainbow gradient (roygb) with a scale relative to values present
in file. In Jmol, 'charge' does the same as 'formalCharge'.

Isosurfaces (solvent, molecular, orbitals...) can be colored uniformly
or using a color map that reflects the value of some property at each
point in the surface (such as molecular electrostatic potential,
distance, etc.).
For these maps all the predefined gradients of
color are available (and the reverse gradients too), using the
'colorScheme' parameter of 'isoSurface' command.